I faced similar issue and I think that LR4 just needs some time to discover the changes. Do you have your photos in DNG?
I have DNG as well as lots of JPG and some CR2, the issue is with all file types. However I didn't notice any status change in LR4 within say 10 minutes. Not sure if it would help to have LR running for hours, I've never tried that. Do you thing that could help?